Merge pull request #3199 from mirpedrol/release-review

Release review [skip changelog]

.github/workflows/create-test-wf.yml

@@ -71,10 +71,6 @@ jobs:
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
-          # echo current directory
-          pwd
-          # echo content of current directory
-          ls -la
           nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results
 
       - name: Upload log file artifact

CHANGELOG.md

@@ -1,6 +1,6 @@
 # nf-core/tools: Changelog
 
-## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-07]
+## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 
 **Highlights**
 

README.md

@@ -21,7 +21,7 @@ For documentation of the internal Python functions, please refer to the [Tools P
 
 ## Installation
 
-For full installation instructions, please see the [nf-core documentation](https://nf-co.re/docs/usage/tools).
+For full installation instructions, please see the [nf-core documentation](https://nf-co.re/docs/nf-core-tools/installation).
 Below is a quick-start for those who know what they're doing:
 
 ### Bioconda

nf_core/components/list.py

@@ -25,7 +25,7 @@ def __init__(
         self.remote = remote
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
 
-    def _configure_repo_and_paths(self, nf_dir_req=True) -> None:
+    def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
         Override the default with nf_dir_req set to False to allow
         info to be run from anywhere and still return remote info

nf_core/components/nfcore_component.py

@@ -5,7 +5,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import Any, List, Optional, Tuple, Union
+from typing import Any, Dict, List, Optional, Tuple, Union
 
 log = logging.getLogger(__name__)
 
@@ -50,7 +50,7 @@ def __init__(
         self.passed: List[Tuple[str, str, Path]] = []
         self.warned: List[Tuple[str, str, Path]] = []
         self.failed: List[Tuple[str, str, Path]] = []
-        self.inputs: List[list[dict[str, dict[str, str]]]] = []
+        self.inputs: List[List[Dict[str, Dict[str, str]]]] = []
         self.outputs: List[str] = []
         self.has_meta: bool = False
         self.git_sha: Optional[str] = None

nf_core/modules/modules_differ.py

@@ -391,8 +391,8 @@ def get_new_and_old_lines(patch):
     def try_apply_single_patch(file_lines, patch, reverse=False):
         """
         Tries to apply a patch to a modified file. Since the line numbers in
-        the patch does not agree if the file is modified, the old and new
-        lines inpatch are reconstructed and then we look for the old lines
+        the patch do not agree if the file is modified, the old and new
+        lines in the patch are reconstructed and then we look for the old lines
         in the modified file. If all hunk in the patch are found in the new file
         it is updated with the new lines from the patch file.